# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 23:38:36 2020
#   Inital geometry file: a 161 line input string
#   Ligand name: N-(methylsulfonyl)-D-phenylalanyl-N-[(1-carbamimidoylpiperidin-4-yl)methyl]-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCC3CCN(CC3)C(N)=N
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 0BM  0BM  N-(methylsulfonyl)-D-phenylalanyl-N-[(1-carbamimidoylpiperidin-4-yl)methyl]-L-prolinamide  ligand  67  33  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0BM
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 0BM  S10   S  S     0   1.340   3.3052   2.1557   0.9377
 0BM  O11   O  OS    0  -0.663   2.8031   1.6334   2.2027
 0BM  O12   O  OS    0  -0.675   2.8929   3.4858   0.5120
 0BM  C13   C  CH3   0  -0.785   5.0769   2.0797   0.9896
 0BM  N9    N  NC1   0  -0.735   2.9378   1.1414  -0.3074
 0BM  C8    C  CH1   0  -0.226   2.8106  -0.2812  -0.0791
 0BM  C15   C  C     0   0.590   1.3380  -0.6748   0.0177
 0BM  O16   O  O     0  -0.492   0.4948  -0.0600  -0.6217
 0BM  C7    C  CH2   0  -0.520   3.4844  -1.0462  -1.2327
 0BM  C6    C  CR6   0   0.137   4.9531  -0.7400  -1.2752
 0BM  C1    C  CR16  0  -0.296   5.4543   0.2560  -2.1079
 0BM  C5    C  CR16  0  -0.304   5.8320  -1.4030  -0.4213
 0BM  C2    C  CR16  0  -0.243   6.8029   0.5863  -2.0865
 0BM  C4    C  CR16  0  -0.240   7.1800  -1.0736  -0.3931
 0BM  C3    C  CR16  0  -0.266   7.6689  -0.0742  -1.2251
 0BM  N17   N  NT    0  -0.478   1.0334  -1.7384   0.7679
 0BM  C21   C  CH1   0  -0.171  -0.3465  -2.1754   0.8858
 0BM  C22   C  C     0   0.563  -1.2434  -1.0603   1.4089
 0BM  O23   O  O     0  -0.490  -0.8507  -0.2542   2.2370
 0BM  C20   C  CH2   0  -0.481  -0.2771  -3.3292   1.8995
 0BM  C19   C  CH2   0  -0.469   1.1583  -3.8266   1.7846
 0BM  C18   C  CH2   0  -0.289   1.9477  -2.5447   1.5693
 0BM  N24   N  NH1   0  -0.649  -2.4995  -1.0967   0.9500
 0BM  C25   C  CH2   0  -0.218  -3.5350  -0.2055   1.4294
 0BM  C26   C  CH1   0  -0.314  -4.8451  -0.4268   0.6884
 0BM  C27   C  CH2   0  -0.421  -4.7500  -0.1063  -0.8004
 0BM  C28   C  CH2   0  -0.274  -6.0934  -0.2615  -1.4986
 0BM  N29   N  NT    0  -0.469  -7.1053   0.5520  -0.8518
 0BM  C30   C  CH2   0  -0.299  -7.2633   0.2456   0.5632
 0BM  C31   C  CH2   0  -0.417  -5.9504   0.4216   1.3079
 0BM  C32   C  C     0   0.553  -8.1788   0.9683  -1.6093
 0BM  N33   N  NH2   0  -0.839  -9.0940   1.7516  -0.9327
 0BM  N34   N  N     0  -0.711  -8.2856   0.6151  -2.8375
 0BM  H113  H  HCH3  0   0.285   5.3916   1.0574   1.1909
 0BM  H213  H  HCH3  0   0.292   5.4768   2.4038   0.0330
 0BM  H313  H  HCH3  0   0.303   5.4168   2.7344   1.7904
 0BM  HN9   H  HNC1  0   0.412   2.2562   1.5375  -0.9466
 0BM  H8    H  HCH1  0   0.290   3.3283  -0.5308   0.8486
 0BM  H17   H  HCH2  0   0.271   3.3211  -2.1190  -1.1039
 0BM  H27   H  HCH2  0   0.273   3.0011  -0.7643  -2.1706
 0BM  H1    H  HCR6  0   0.247   4.7821   0.7807  -2.7756
 0BM  H5    H  HCR6  0   0.248   5.4586  -2.1856   0.2307
 0BM  H2    H  HCR6  0   0.255   7.1772   1.3639  -2.7403
 0BM  H4    H  HCR6  0   0.256   7.8482  -1.5973   0.2781
 0BM  H3    H  HCR6  0   0.255   8.7192   0.1856  -1.2043
 0BM  H21   H  HCH1  0   0.280  -0.7077  -2.5361  -0.0828
 0BM  H120  H  HCH2  0   0.253  -0.4608  -2.9576   2.9098
 0BM  H220  H  HCH2  0   0.268  -1.0196  -4.0962   1.6864
 0BM  H119  H  HCH2  0   0.261   1.4919  -4.3717   2.6661
 0BM  H219  H  HCH2  0   0.248   1.2686  -4.4818   0.9185
 0BM  H118  H  HCH2  0   0.255   2.8876  -2.7327   1.0516
 0BM  H218  H  HCH2  0   0.255   2.1745  -2.0500   2.5179
 0BM  HN24  H  HNH1  0   0.401  -2.7489  -1.8069   0.2802
 0BM  H125  H  HCH2  0   0.240  -3.6927  -0.3625   2.5013
 0BM  H225  H  HCH2  0   0.230  -3.2136   0.8326   1.3026
 0BM  H26   H  HCH1  0   0.232  -5.1307  -1.4822   0.7994
 0BM  H127  H  HCH2  0   0.221  -4.3935   0.9215  -0.9268
 0BM  H227  H  HCH2  0   0.236  -4.0282  -0.7547  -1.3027
 0BM  H128  H  HCH2  0   0.253  -6.0075   0.0437  -2.5384
 0BM  H228  H  HCH2  0   0.208  -6.3886  -1.3210  -1.5010
 0BM  H130  H  HCH2  0   0.255  -8.0229   0.8803   1.0117
 0BM  H230  H  HCH2  0   0.219  -7.6101  -0.7910   0.6857
 0BM  H131  H  HCH2  0   0.240  -6.1008   0.1457   2.3546
 0BM  H231  H  HCH2  0   0.224  -5.6613   1.4775   1.2899
 0BM  H133  H  HNH2  0   0.385  -8.7153   2.3913  -0.2512
 0BM  H233  H  HNH2  0   0.385  -9.7629   2.2120  -1.5295
 0BM  H134  H  H     0   0.316  -9.0588   1.0982  -3.2805

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 0BM  C1   C2    aromatic  1.389  0.020  1.389
 0BM  C1   C6    aromatic  1.392  0.020  1.392
 0BM  C1   H1    single    0.930  0.020  1.080
 0BM  C2   C3    aromatic  1.389  0.020  1.389
 0BM  C2   H2    single    0.930  0.020  1.080
 0BM  C3   C4    aromatic  1.389  0.020  1.389
 0BM  C3   H3    single    0.930  0.020  1.080
 0BM  C4   H4    single    0.930  0.020  1.080
 0BM  C5   C4    aromatic  1.388  0.020  1.388
 0BM  C5   H5    single    0.930  0.020  1.080
 0BM  C6   C5    aromatic  1.393  0.020  1.393
 0BM  C7   C6    single    1.501  0.020  1.501
 0BM  C7   H17   single    0.970  0.020  1.090
 0BM  C7   H27   single    0.970  0.020  1.090
 0BM  C8   C7    single    1.539  0.020  1.539
 0BM  C8   H8    single    0.970  0.020  1.090
 0BM  N9   C8    single    1.446  0.020  1.446
 0BM  N9   S10   single    1.647  0.020  1.647
 0BM  N9   HN9   single    0.890  0.020  1.040
 0BM  S10  O11   double    1.458  0.020  1.458
 0BM  O12  S10   double    1.456  0.020  1.456
 0BM  C13  S10   single    1.774  0.020  1.774
 0BM  C13  H113  single    0.970  0.020  1.090
 0BM  C13  H213  single    0.970  0.020  1.090
 0BM  C13  H313  single    0.970  0.020  1.090
 0BM  C15  N17   single    1.337  0.020  1.337
 0BM  C15  C8    single    1.527  0.020  1.527
 0BM  O16  C15   double    1.224  0.020  1.224
 0BM  N17  C18   single    1.459  0.020  1.459
 0BM  C18  H118  single    0.970  0.020  1.090
 0BM  C18  H218  single    0.970  0.020  1.090
 0BM  C19  C18   single    1.521  0.020  1.521
 0BM  C19  H119  single    0.970  0.020  1.090
 0BM  C19  H219  single    0.970  0.020  1.090
 0BM  C20  C19   single    1.523  0.020  1.523
 0BM  C20  H120  single    0.970  0.020  1.090
 0BM  C20  H220  single    0.970  0.020  1.090
 0BM  C21  C20   single    1.537  0.020  1.537
 0BM  C21  N17   single    1.452  0.020  1.452
 0BM  C21  H21   single    0.970  0.020  1.090
 0BM  C22  C21   single    1.524  0.020  1.524
 0BM  C22  O23   double    1.221  0.020  1.221
 0BM  N24  C22   single    1.338  0.020  1.338
 0BM  N24  HN24  single    0.860  0.020  1.020
 0BM  C25  N24   single    1.448  0.020  1.448
 0BM  C25  H125  single    0.970  0.020  1.090
 0BM  C25  H225  single    0.970  0.020  1.090
 0BM  C26  C25   single    1.521  0.020  1.521
 0BM  C26  C31   single    1.525  0.020  1.525
 0BM  C26  H26   single    0.970  0.020  1.090
 0BM  C27  C26   single    1.526  0.020  1.526
 0BM  C27  H127  single    0.970  0.020  1.090
 0BM  C27  H227  single    0.970  0.020  1.090
 0BM  C28  C27   single    1.522  0.020  1.522
 0BM  C28  N29   single    1.451  0.020  1.451
 0BM  C28  H128  single    0.970  0.020  1.090
 0BM  C28  H228  single    0.970  0.020  1.090
 0BM  N29  C30   single    1.456  0.020  1.456
 0BM  C30  C31   single    1.520  0.020  1.520
 0BM  C30  H130  single    0.970  0.020  1.090
 0BM  C30  H230  single    0.970  0.020  1.090
 0BM  C31  H131  single    0.970  0.020  1.090
 0BM  C31  H231  single    0.970  0.020  1.090
 0BM  C32  N29   single    1.378  0.020  1.378
 0BM  C32  N33   single    1.382  0.020  1.382
 0BM  N33  H133  single    0.890  0.020  1.040
 0BM  N33  H233  single    0.890  0.020  1.040
 0BM  N34  C32   double    1.282  0.020  1.282
 0BM  N34  H134  single    0.890  0.020  1.040

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 0BM  N9    S10  C13   102.62  3.000
 0BM  C13   S10  O12   109.29  3.000
 0BM  N9    S10  O12   106.16  3.000
 0BM  C13   S10  O11   107.65  3.000
 0BM  O12   S10  O11   118.91  3.000
 0BM  N9    S10  O11   111.01  3.000
 0BM  H313  C13  H213  110.69  3.000
 0BM  H313  C13  H113  109.79  3.000
 0BM  H213  C13  H113  109.67  3.000
 0BM  H313  C13  S10   107.91  3.000
 0BM  H213  C13  S10   109.21  3.000
 0BM  H113  C13  S10   109.54  3.000
 0BM  HN9   N9   C8    115.10  3.000
 0BM  HN9   N9   S10   112.67  3.000
 0BM  C8    N9   S10   120.39  3.000
 0BM  H8    C8   C7    108.41  3.000
 0BM  H8    C8   C15   110.15  3.000
 0BM  C7    C8   C15   109.96  3.000
 0BM  C15   C8   N9    110.38  3.000
 0BM  H8    C8   N9    108.51  3.000
 0BM  C7    C8   N9    109.39  3.000
 0BM  N17   C15  O16   122.41  3.000
 0BM  O16   C15  C8    120.11  3.000
 0BM  N17   C15  C8    117.41  3.000
 0BM  H27   C7   H17   106.77  3.000
 0BM  H27   C7   C6    110.86  3.000
 0BM  H17   C7   C6    110.48  3.000
 0BM  H27   C7   C8    108.76  3.000
 0BM  H17   C7   C8    109.52  3.000
 0BM  C6    C7   C8    110.37  3.000
 0BM  C5    C6   C1    118.69  3.000
 0BM  C5    C6   C7    120.19  3.000
 0BM  C1    C6   C7    121.03  3.000
 0BM  H1    C1   C2    119.80  3.000
 0BM  H1    C1   C6    119.47  3.000
 0BM  C2    C1   C6    120.72  3.000
 0BM  H5    C5   C4    119.56  3.000
 0BM  H5    C5   C6    119.63  3.000
 0BM  C4    C5   C6    120.81  3.000
 0BM  H2    C2   C3    120.04  3.000
 0BM  H2    C2   C1    119.82  3.000
 0BM  C3    C2   C1    120.14  3.000
 0BM  H4    C4   C3    120.15  3.000
 0BM  H4    C4   C5    119.82  3.000
 0BM  C3    C4   C5    120.02  3.000
 0BM  H3    C3   C4    120.18  3.000
 0BM  H3    C3   C2    120.20  3.000
 0BM  C4    C3   C2    119.62  3.000
 0BM  C18   N17  C21   112.62  3.000
 0BM  C21   N17  C15   120.10  3.000
 0BM  C18   N17  C15   127.24  3.000
 0BM  H21   C21  C20   110.54  3.000
 0BM  H21   C21  C22   110.53  3.000
 0BM  C20   C21  C22   110.45  3.000
 0BM  C22   C21  N17   111.53  3.000
 0BM  H21   C21  N17   109.93  3.000
 0BM  C20   C21  N17   103.68  3.000
 0BM  N24   C22  O23   123.56  3.000
 0BM  N24   C22  C21   114.52  3.000
 0BM  O23   C22  C21   121.80  3.000
 0BM  H220  C20  H120  107.82  3.000
 0BM  H220  C20  C19   113.44  3.000
 0BM  H120  C20  C19   109.83  3.000
 0BM  H220  C20  C21   111.65  3.000
 0BM  H120  C20  C21   110.31  3.000
 0BM  C19   C20  C21   103.76  3.000
 0BM  H219  C19  H119  108.11  3.000
 0BM  H219  C19  C18   109.95  3.000
 0BM  H119  C19  C18   112.18  3.000
 0BM  H219  C19  C20   110.55  3.000
 0BM  H119  C19  C20   113.02  3.000
 0BM  C18   C19  C20   102.98  3.000
 0BM  H218  C18  H118  108.14  3.000
 0BM  H218  C18  C19   111.48  3.000
 0BM  H118  C18  C19   111.70  3.000
 0BM  C19   C18  N17   102.61  3.000
 0BM  H218  C18  N17   110.88  3.000
 0BM  H118  C18  N17   112.02  3.000
 0BM  HN24  N24  C25   118.48  3.000
 0BM  C25   N24  C22   122.76  3.000
 0BM  HN24  N24  C22   118.67  3.000
 0BM  H225  C25  H125  106.97  3.000
 0BM  H225  C25  C26   109.54  3.000
 0BM  H125  C25  C26   109.39  3.000
 0BM  C26   C25  N24   111.41  3.000
 0BM  H225  C25  N24   109.60  3.000
 0BM  H125  C25  N24   109.81  3.000
 0BM  H26   C26  C31   107.75  3.000
 0BM  H26   C26  C27   108.45  3.000
 0BM  C31   C26  C27   108.95  3.000
 0BM  C27   C26  C25   113.02  3.000
 0BM  H26   C26  C25   108.31  3.000
 0BM  C31   C26  C25   110.20  3.000
 0BM  H227  C27  H127  106.79  3.000
 0BM  H227  C27  C28   108.16  3.000
 0BM  H127  C27  C28   109.27  3.000
 0BM  C28   C27  C26   111.79  3.000
 0BM  H227  C27  C26   111.42  3.000
 0BM  H127  C27  C26   109.27  3.000
 0BM  H228  C28  H128  106.83  3.000
 0BM  H228  C28  N29   110.73  3.000
 0BM  H128  C28  N29   108.91  3.000
 0BM  H228  C28  C27   109.65  3.000
 0BM  H128  C28  C27   109.91  3.000
 0BM  N29   C28  C27   110.73  3.000
 0BM  C32   N29  C30   120.87  3.000
 0BM  C32   N29  C28   117.88  3.000
 0BM  C30   N29  C28   113.01  3.000
 0BM  H230  C30  H130  106.51  3.000
 0BM  H230  C30  C31   109.08  3.000
 0BM  H130  C30  C31   109.51  3.000
 0BM  H230  C30  N29   109.92  3.000
 0BM  H130  C30  N29   110.73  3.000
 0BM  C31   C30  N29   110.98  3.000
 0BM  H231  C31  H131  107.20  3.000
 0BM  H231  C31  C30   109.37  3.000
 0BM  H131  C31  C30   108.74  3.000
 0BM  H231  C31  C26   109.78  3.000
 0BM  H131  C31  C26   110.39  3.000
 0BM  C30   C31  C26   111.27  3.000
 0BM  N34   C32  N33   124.75  3.000
 0BM  N34   C32  N29   120.54  3.000
 0BM  N33   C32  N29   114.71  3.000
 0BM  H233  N33  H133  111.08  3.000
 0BM  H233  N33  C32   114.12  3.000
 0BM  H133  N33  C32   116.22  3.000
 0BM  H134  N34  C32   110.54  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 0BM  CONST_01  C3    C2   C1   C6     0.00   0.0  0
 0BM  CONST_02  C3    C4   C5   C6     0.00   0.0  0
 0BM  CONST_03  C4    C3   C2   C1     0.00   0.0  0
 0BM  CONST_04  C4    C5   C6   C1     0.00   0.0  0
 0BM  CONST_05  C2    C3   C4   C5     0.00   0.0  0
 0BM  CONST_06  C2    C1   C6   C5     0.00   0.0  0
 0BM  CONST_07  C2    C1   C6   C7   180.00   0.0  0
 0BM  CONST_08  C4    C5   C6   C7   180.00   0.0  0
 0BM  CONST_09  H2    C2   C1   C6   180.00   0.0  0
 0BM  CONST_10  H4    C4   C5   C6   180.00   0.0  0
 0BM  CONST_11  H3    C3   C2   C1   180.00   0.0  0
 0BM  CONST_12  H5    C5   C6   C1   180.00   0.0  0
 0BM  CONST_13  H1    C1   C6   C5   180.00   0.0  0
 0BM  CONST_14  C18   N17  C15  C8     0.00   0.0  0
 0BM  CONST_15  C21   N17  C15  C8   180.00   0.0  0
 0BM  CONST_16  C18   N17  C15  O16  180.00   0.0  0
 0BM  CONST_17  C21   N17  C15  O16    0.00   0.0  0
 0BM  CONST_18  N33   C32  N29  C28  180.00   0.0  0
 0BM  CONST_19  N34   C32  N29  C28    0.00   0.0  0
 0BM  CONST_22  C25   N24  C22  C21  180.00   0.0  0
 0BM  CONST_23  HN24  N24  C22  C21    0.00   0.0  0
 0BM  CONST_25  H233  N33  C32  N29  180.00   0.0  0
 0BM  CONST_26  H134  N34  C32  N29  180.00   0.0  0
 0BM  CONST_27  C25   N24  C22  O23    0.00   0.0  0
 0BM  Var_01    C20   C19  C18  N17  -35.05  30.0  1
 0BM  Var_02    C18   C19  C20  C21   37.00  30.0  1
 0BM  Var_03    C19   C18  N17  C21   20.76  30.0  1
 0BM  Var_04    N29   C30  C31  C26  -56.03  30.0  1
 0BM  Var_05    N29   C28  C27  C26   55.48  30.0  1
 0BM  Var_06    C30   N29  C28  C27  -57.15  30.0  1
 0BM  Var_07    C31   C30  N29  C28   57.71  30.0  1
 0BM  Var_08    C1    C6   C7   C8   -95.07  30.0  2
 0BM  Var_09    C26   C25  N24  C22  177.36  30.0  1
 0BM  Var_10    C8    N9   S10  O11  -29.49  30.0  2
 0BM  Var_11    H113  C13  S10  O11   56.27  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 0BM  chir_01  C8   C7   N9   C15  negativ
 0BM  chir_02  C21  N17  C20  C22  negativ
 0BM  chir_03  C26  C25  C31  C27  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 0BM  plan-1  C7    0.020
 0BM  plan-1  C6    0.020
 0BM  plan-1  C1    0.020
 0BM  plan-1  C5    0.020
 0BM  plan-1  C2    0.020
 0BM  plan-1  C4    0.020
 0BM  plan-1  C3    0.020
 0BM  plan-1  H1    0.020
 0BM  plan-1  H5    0.020
 0BM  plan-1  H2    0.020
 0BM  plan-1  H4    0.020
 0BM  plan-1  H3    0.020
 0BM  plan-2  C21   0.020
 0BM  plan-2  C22   0.020
 0BM  plan-2  O23   0.020
 0BM  plan-2  N24   0.020
 0BM  plan-2  C25   0.020
 0BM  plan-2  HN24  0.020
 0BM  plan-3  C8    0.020
 0BM  plan-3  C15   0.020
 0BM  plan-3  O16   0.020
 0BM  plan-3  N17   0.020
 0BM  plan-3  C21   0.020
 0BM  plan-3  C18   0.020
 0BM  plan-4  C28   0.020
 0BM  plan-4  N29   0.020
 0BM  plan-4  C30   0.020
 0BM  plan-4  C32   0.020
 0BM  plan-4  N33   0.020
 0BM  plan-4  N34   0.020
 0BM  plan-4  H133  0.020
 0BM  plan-4  H233  0.020
 0BM  plan-4  H134  0.020

